If you're thinking random battles like DQ2's ship where you get it ~20% through the game, then have to fight the same weak ass, pathetic enemies for the remaining 80%, then hell no. I wouldn't even have random battles on the ship at all.
But if you have some optional water dungeons in mind, or a few wandering critters who pick a fight when touched, that's cool. Actual sea travel should be safe, or else the long distances a player has to traverse quickly become aggravating.
On the subject of an upgradeable ship, I'm all for it. I've mused on the idea of a ship doubling as the player's headquarters, where their personal inn and store keepers set up shop once you 'recruit' them.